Interpretive Summary: This manuscript describes research to define molecular markers for fungi studied for biological control of problem weeds, such as thistles. We are identifying and testing the specificity of markers that will help us to follow the biological control agents once they are released into the environment. This research will help regulatory agencies to assess the risk of such releases, and will allow researchers to track the biological control agent in the field

Technical Abstract:
We evaluated the polymorphism between isolates in the internal transcribed spacer (ITS) regions of ribosomal DNA to find genetic markers for isolates of Puccinia carduorum currently under evaluation for biological control of Carduus thoermeri (musk thistle). A 663-670 bp region, including the 5.8S gene and the two flanking ITS regions, was amplified by polymerase chain reaction from and digested with the restriction enzymes Alu I, Dra I, Eco RI, Hinf I, Mse I and Taq I. Unique patterns were produced upon restriction of ITS DNA amplified from four separate Puccinia spp. Fourteen isolates of P. carduorum from four species of Carduus weed hosts showed two different patterns that correlated to the host plant origin. Restriction patterns of P. carduorum isolates from C. acanthoides and C. thoermeri were distinct from those of P. carduorum from C. tenuiflorus and C. pycnocephalus. We concluded that isolates of P. carduorum from different hosts can be differentiated whereas those from the same host are indistinguishable by this technique